5/1/23, 10:55 AM Syllabus for BIPN 164 - Comp Models in Neuro - Benna [SP23]

Course Syllabus

Link to pdf version: BIPN164_Sp23_Aljadeff_Benna_Syllabus.pdf

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BIPN 164: Computational Models and Theories in Neuroscience

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Spring Quarter 2023

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In-person lectures: Tata Hall, Room 3201, TuTh 5-6:20pm

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Instructors: Johnatan Aljadeff, PhD; Marcus Benna, PhD

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Email: aljadeff@ucsd.edu (mailto:aljadeff@ucsd.edu) ; mbenna@ucsd.edu

(mailto:mbenna@ucsd.edu)

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Office Hours:

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Aljadeff, Mondays 3-4pm. CNCB 107 (Weeks 1-4, 9-10)

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Benna, TBD (Weeks 5-10)

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Course IAs:

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TA: Meg Robinson (Wednesday discussions); Chandramouli Rajagopalan (Friday discussions)

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Email: m5robinson@ucsd.edu (mailto:m5robinson@ucsd.edu) ; crajagopalan@ucsd.edu

(mailto:crajagopalan@ucsd.edu)

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Office Hours:

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Robinson, Thursdays 3:30-4:30pm. FAH 2101 or https://ucsd.zoom.us/j/3688622604

(https://ucsd.zoom.us/j/3688622604)

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Rajagopalan, TBD

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Course Description:

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This course covers mathematical models of neurons, synapses, and neural networks. We will
introduce theoretical frameworks of brain activity and function to understand neural computation
and control of behavior. We will discuss network dynamics, synaptic plasticity, learning and
memory. Students will apply modeling approaches to address scientific questions and make
predictions for experiments.

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Course Outcomes:

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The goal of this course is to give students the necessary background and skills to understand how
modeling approaches are applied to problems in neuroscience. Students will learn how to identify
the type of model appropriate for specific scientific questions, neuronal systems and experimental
datasets. The students will gain experience in how to extract experimentally testable predictions
from computational models of neuronal systems at the single neuron and the network level.

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Course Requirements:

Readings:

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The following two books cover the course material:

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Gerstner, W., Kistler, W. M., Naud, R., & Paninski, L. (2014). Neuronal dynamics: From single
neurons to networks and models of cognition. Cambridge University Press.
ebook link: https://neuronaldynamics.epfl.ch/online/index.html
(https://neuronaldynamics.epfl.ch/online/index.html)
Dayan, P., & Abbott, L. F. (2005). Theoretical neuroscience: computational and mathematical
modeling of neural systems. MIT press.
ebook link: https://boulderschool.yale.edu/sites/default/files/files/DayanAbbott.pdf
(https://boulderschool.yale.edu/sites/default/files/files/DayanAbbott.pdf)

These books differ primarily in the mathematical level of the presentation. Overall Dayan & Abbott
is easier to understand, while Gerstner et al. provide a more complete and up-to-date view of the
field. Both books are available for free as ebooks via the library. The instructors will therefore
assign reading from either book, on a topic-by-topic basis. When assigned, course readings must
be completed before lecture. Lectures will draw heavily from the readings, so please come
prepared to answer or ask questions about it.

Another useful resource are the materials of the Neuromatch Academy (academy.neuromatch.io
(https://academy.neuromatch.io/) ). Students are encouraged to consult these lecture materials
and worked-out exercises, which will help with this course’s homework assignments.

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Attendance:

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Attendance is highly encouraged at every lecture, as the homework and final exam will include
materials covered in lecture that may not be explicitly mentioned in the readings. A significant

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portion of the lecture will be given on the white-board (not on slides). The course will not be
podcasted.

The most effective way of succeeding in this course is attending the lectures and taking notes.
Importantly, the lectures will include materials that may not be contained in the readings, so it will
be beneficial to be present and engage in active listening, note taking and participation.

Please note: It is the students’ responsibility to attend all classes and to find out (from a peer)
about material covered in any classes they may have missed.

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Course Website:

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Please check the course website on Canvas at least three times a week for updates,
announcements, and ongoing class operations. Checking updates is your responsibility.
Please make sure you are aware of the information available on Canvas when preparing for class
or other parts of the course.

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Email Policy:

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Email is a vital way to communicate with your professors, the course IAs and classmates. We
highly suggest you check your email at least three times a week, as we will be sending important
reminders and announcements to your email. This is an easy way to ensure you do not miss
anything. It is also a great way to get in contact with us or the IAs with any questions about
information not already accessible (e.g., not included on the syllabus or Canvas Page). Please
note that it may take up to 48 hours to receive a response. Always include BIPN 164 in the subject
of your email.

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Course Assessments:

Homework Assignments:

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The Homework Assignments are aimed at assessing your understanding of the course material to
date, your ability to apply the material you learned, and to present it in a professional and clear

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way. You are encouraged to consult with online resources, including the Neuromatch Academy
mentioned above, and with your classmates when working on the assignments. Homework will be
assigned to groups of 2-4 students, to accommodate complementary backgrounds in biology,
mathematics and programming.

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We will ask you to fill out a questionnaire on your background at the beginning of the course, to
make these pairings effective and productive. It is important to be honest in filling out these
questionnaires. Your responses will not affect your grade in any way. Misrepresentation of your
background will make it extremely difficult to form effective teams for the homework assignments.
However, even when work on the assignments is done in pairs/groups, each student must
write up and submit their own homework, which they will be graded on. Homework solutions
will be covered in the discussion section by the IAs in the following weeks, to ensure all course
concepts are thoroughly understood.

Quizzes:

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Quizzes consisting of questions related to the lecture material will be assigned in between
homework problems sets. They should be done individually.

Final Exam:

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The final is designed to evaluate your mastery of the course concepts and material. It will largely
be based on a short answer and problem-solving format, drawing from lectures (including possible
guest lectures), homework, and course readings. You should not consult with your peers, the
internet, course slides, readings, or your lecture notes while taking the exam. You will be
allowed to use one page of notes in the exam.

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The exam will be given in person and will be timed. You will only be allowed one attempt to take
the final. The final will be given on 6/15/2023 from 7pm-10pm.

Section/Review Sessions:

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An optional section led by the IAs will be held each week. We encourage you to attend these
sections to go over any questions or concerns you may have. While the section is intended to help

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you with homework assignments and preparation for the exam, you will need to come with
questions or points for clarification. It will not be a lecture that summarizes each week’s material.

Grading/Re-grading Policy:

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For the course assessments, we will ensure that grading is as consistent and fair as possible, and
if any grading errors should occur we will do our best to correct them. However, please do not ask
for something to be regraded simply because you feel you deserve a higher grade, without a clear
description of where you think there was an error. You are responsible for earning an A in this
class. Earning an A will require: 1) attending lectures 2) actively participating in and taking notes
on lectures and readings 3) submitting homework assignments on time 4) coming to office hours if
you do not understand the material and 5) preparing for your exams (studying).

Late Assignment Policy:

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Deadlines are an integral part of professional and academic life, and there are deadlines for every
assignment in this course. Assignments will lose 10% of the available points for each day they are
late.

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Grading Breakdown:

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Assessment Grade Percentage

4 homework assignments 15% x 4 = 60%

4 take-home short quizzes 4% x 4 = 16%

Final Exam 24%

Extra credit opportunities 1-3%

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Grade Scale:

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Letter Grade Percentage

A+ 97-100%

A 93-96.99%

A- 90-92.99%

B+ 87-89.99%

B 83-86.99%

B- 80-82.99%

C+ 77-79.99%

C 73-76.99%

C- (pass grade) 70-72.99%

D (fail grade) 60-69.99%

F (fail grade) 0-59.99%

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Accommodations:

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Students requesting accommodations for this course due to a disability must provide a current
Authorization for Accommodation (AFA) letter issued by the Office for Students with Disabilities
(OSD, https://osd.ucsd.edu/ (https://osd.ucsd.edu/) ). Students should present their AFA letters to

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the instructors and to the OSD Liaison at the Division of Biological Sciences in advance so that
accommodations may be arranged.

If you will need to reschedule exams due to academic or sports exceptions, please provide the
letter to the Instructors and the Teaching Assistant as soon as possible (preferably before the end
of Week 3).

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Classroom Environment:

Professionalism Policy:

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Please adhere to all university policy and proper classroom etiquette. Those who are not following
these guidelines will be asked to leave, in order to maintain the learning environment for other
students. Please arrive on time, be attentive, and respectful to your instructor, guest lecturers, IAs,
and fellow classmates. Be mindful of how much time and space you are occupying. Try not to
interrupt others when they have the floor. Do not expect to feel comfortable with the material at all
times. Expect this course to challenge you. UCSD recognizes the inherent dignity of all individuals
and promotes respect for all people. Hostility toward other students will not be tolerated. Free
speech does not permit harassment, intimidation, threats, or other behaviors that impede
the learning of other students or the work of instructors, guest lecturers, and IAs.

You may use your laptop or tablets to take notes during lectures. However, this is strictly for note
taking or class activities. If we notice that you are using it for anything other than class-related
activities, we may ask you to put it away. Cell phones should be silenced before class and not
used at all during lecture.

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Principles of Community:

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UCSD is dedicated to learning, teaching, and serving society through education, research, and
public service. Students are encouraged to be creative and are rewarded for individual as well as
collaborative achievements. To foster the best possible working and learning environment, UC San
Diego strives to maintain a climate of fairness, cooperation, and professionalism. UCSD students
are expected to practice these basic principles as individuals and in groups. Please review and
abide by the UCSD Principles of Community: https://ucsd.edu/about/principles.html

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(https://ucsd.edu/about/principles.html) . These specifically include 1) fostering inclusiveness,

respect, and a welcoming environment and 2) promoting collaborative attitudes and actions.

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We support the education and social advancement of all students, regardless of their
immigration status, religion, race, ethnicity, gender identity, or any other social factors that
could be used to limit their life opportunities. We are here to help you succeed, and we will do
what we can to make that happen.

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Schedule:

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Week and Weekly

Daily Topic Readings
Focus

Week 1 Introductions,
(Aljadeff): Syllabus Review,
Single Course Expectations,
neuron Questionnaire;
models
Why is modeling
important for
Tue (4/4) No readings
understanding the
brain?

What kind of models

will be (and will not
be) discussed in this
course?

Thu (4/6) Hodgkin and Huxley: D&A Chapter II 5

ion channels and GKN&P Chapter 2

nonlinear
conductance
equations
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From the Hodgkin-

Huxley equations to
Tue
spiking activity
(4/11)
(oscillations).

The neuron’s input-

Week 2 output relationship
(Aljadeff):
D&A Chapter II 5
Mathematical primer
Single
Thu on dimensionality GKN&P Chapter 4
neuron
(4/13): reduction (principal
models
component analysis)
Deadline
to add
the From Hodgkin-Huxley
course oscillations to
simplified models.

Viewing each synapse D&A Chapter II 5.8

as a dynamical
system: (partially covers material)
Tue
(4/18) Models of resource
Week 3
depletion, facilitation, Tsodyks, M., Pawelzik, K., & Markram, H. (1998).
(Aljadeff):
adaptation, and short Neural networks with dynamic synapses. Neural
Single term plasticity
computation, 10(4), 821-835.
synapse
models Approaches for
studying neural https://doi.org/10.1162/089976698300017502
Thu
network activity: what (https://doi.org/10.1162/089976698300017502)
(4/20)
is a mean-field
(Challenging but highly recommended reading)
theory?

Week 4 Connectivity motifs

(Aljadeff): Tue
(4/25) Connectivity degree
Network distributions
connectivity
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Thu Connectomics in
(4/27): neuroscience:

Deadline What have we learned

to Drop from extracting the
without a wiring diagram of a
“W” neural circuit?

Firing rate models,

Tue (5/2) feedforward vs. Background material: GKN&P Chapters 12 & 15
Week 5 recurrent networks.

(Benna):
Continuously labeled
Network networks, selective D&A Chapter 7.1-7.3
dynamics Thu (5/4): amplification, input
integration, gain Mathematical Appendix A.3
modulation.

Excitation/inhibition
Tue (5/9) balance, network D&A Chapter 7.4-7.9
stability, attractors.
Week 6
(Benna):
Perception, learned
Network behavior and
dynamics Thu
cognition: perceptual GKN&P Chapters 16 & 18
(5/11):
decision making and
cortical field models.

Autoassociative
Tue
memory and Hopfield GKN&P Chapter 17
Week 7 (5/16)
networks.
(Benna):

Synaptic Single synapse

plasticity Thu dynamics, Hebbian &
D&A Chapter 8.1-8.2
(5/18) covariance learning,
Oja’s rule.

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Unsupervised learning
at the network level, D&A Chapter 8.3
Week 8 Tue
mutual inhibition,
(Benna): (5/23) GKN&P Chapter 19
PCA. (Similarity
Synaptic matching?)
plasticity
Thu Supervised learning
D&A Chapter 8.4-8.7
(5/25) and the perceptron.

Supervised learning
using
Tue
backpropagation and TBD
(5/30)
Week 9 biologically plausible
(Benna): approximations.

Advanced
If time permits:
topics
reinforcement
D&A Chapter 9.1-9.3, or
Thu (6/1) learning, or complex
https://arxiv.org/pdf/1706.04946.pdf
synapses for efficient
long-term memory.

From a steady state

view of neural activity
Week 10 Tue (6/6)
to transient
(Aljadeff):
dynamics.
Advanced
topics and
Transient brain
exam review
Thu (6/8) dynamics and final
exam review

Thu
Final Exam 7-10pm, location TBD
(6/15)

Course Summary:
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Date Details Due

Fri Apr 21, 2023  Homework Assignment 1: due by 8pm

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Tue Apr 25, 2023  Quiz 1, lectures 1-6 due by 11:59pm

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Fri May 5, 2023  Homework Assignment 2: due by 8pm

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